The Orb of Darkness
by Fortellint
Summary: Due to a strange mistake, Ash is thrown into Kalos along with Mewtwo. Once there, they quickly discover the hidden secret of an evil that killed Arceus...
1. An Ancient Betrayal

**Just a note: I will not be using Zygarde because it messes up the roles of the trio in this story.**

In the beginning of the World, when Arceus created life, he gave the realms of sea, land, and sky to His three sons and gave them more to help them rule. He created the humans and Pokémon to show His sons that, no matter how small you are, you can do anything.

His sons ruled Pokéarth, as it came to be called, wisely for thousands of years.

Everything changed when Arceus grew weak and ill.

_''Father, what is wrong?'' Xerneas asked Arceus, who was laying on the altar in the Hall of Origin, his crest the sickly grey of Mystery Forme, a Type only reserved for the God's dying days._

_''_**My Life...Plates have been...poisoned.**_'' said the legend weakly, unable to even sit up. He was laying down with his legs overlapping, in the same way as a common Ponyta or Rattata would die if it had been shot by an arrow. Xerneas grit his teeth in anger. The corvid Legendary couldn't bear to watch his Father, Creator, and friend die in such a shameful way._

_''Who did it?'' Xerneas asked, bowing his head down and sniffing the Life Plates, which lay at a greying pile at Arceus's head crest. He could sense no power coming from them now._

_Arceus looked at him. ''_**One...of...you...three...**_'' he said. A spasm of pain forced him to curl into a ball, revealing a red orb that had been hidden under his body. Arceus screamed in agony, but managed to open his eye one more time and look at Xerneas. '' _**I can...not...be saved...Xerneas...Find...the only...one who can...help...Long...from now...a...human...with the...heart...of a Legendary...**_'' His voice trailed off, his eye closed, and his head relaxed on the stone floor._

_With that, Arceus, the father of Xerneas, the Lord of the Land, Yveltal, Lord of the Skies, and Zriece, Lord of the Sea and the eldest of the trio, as well as all dimensions, passed away._

_Xerneas backed away and bowed his head to the ground in respect, and turned away. He would give Arceus the honor of fading without an observer._

_When he looked back, all that was left of Arceus was the red orb. Xerneas picked it up with one antler, turned, and walked angrily out of the Hall of Origin. He would have to speak with Yveltal for killing their Father..._

After that, the Land and Sky fought, creating all kinds of disasters to the world below. Zriece stayed neutral, as he was the wisest, but he cringed every time his brothers' fighting entered his realm and caused hurricanes and tsunamis.

During one of those battles, Yveltal's red orb of power was lost somewhere on the lands below. Its power hid it from Xerneas, so he couldn't find and destroy it.


	2. Kalos Region

''Sect.'' the Shiny Genesect told the other four. ''Gene gen sec genesect.''

''Genesect.'' the others said, simultaneously using their Techno Boosts on Ash and his friends.

''Pikachu, Electro Ball!'' Ash Ketchum called. Pikachu created the yellow sphere on his tail, then launched it at the red Genesect in front.

The Electro Ball hit with a sharp metallic clink. The Shiny Genesect whirled around at him. It now had a dent covering one headlight-like eye. It took a moment to start a Techno Boost, then shutting its Drive off to block it. The move exploded inside its head, pushing the dent back out but unaffecting the (microchip? brain? parasite [ants have this]?) within.

The Genesect's eyes flashed green, and it Bug Buzzed Pikachu until he fainted.

''Pikachu!'' Ash said, running to the wounded Pokémon.

''Ash! Behind you!'' Iris called before a Genesect grabbed hold of her from behind transformed, and flew off, joining another who was holding Cilan.

Ash whirled around, and the Shiny Genesect's arm blade missed his eye by a hair-width.

_How am I going to beat it? It's got two more friends, and it has Extremespeed._ Ash thought, sending out Krookodile.

''Krookodile, Rock Tomb!'' Ash called.

''Krokodile!'' Krookodile called, crossing his arms, his eyes glowing black.

Rock jutted out and around the three Genesect, enclosing them completely, but the Bug-Steel-Types broke through and all used Techno Boost on Krookodile. He was out as well.

That was Ash's last Pokémon. He knew that now, hope was lost for him and Pikachu. He knew that he had angered the Shiny Genesect to the point that it would kill, not capture, him.

Yet he still protected Pikachu as the Legendary Pokémon advanced.

Their Drives lit up as their Techno Boosts activated. Ash closed his eyes in surrender.

He felt a rush of air, and opened his eyes. He shrieked involuntarily. Holding him and Pikachu was a white being with a purple tail-like crest on its head, a humanoid body with a ridge on its sternum, and stretched pea-shaped fingers and toes. It was teleporting them somewhere, but his shriek startled it, and it tumble out of the Teleport, carrying them with it.

It let go of them before they all collided with the ground. Ash and Pikachu landed on their backs, winded but unhurt. The being sailed over them, landing facefirst and skidding along the ground like a meteor.

It got up and spit grass and dirt from its mouth. It opened its eyes, revealing the reddish-amber irises within.

''W-who are you?'' Ash asked, automatically picking up Pikachu and hiding him from view. He recognized this being, but he couldn't remember where...

The being stood up. ''_I'm a friend of yours. This is just my body with a few of my own modifications._'' it said with a telepathic voice that Ash recognized.

The being's form shimmered, and it shrank to around six feet tall. Ash gasped when he recognized the lavender-colored Psychic-Type. The first time he had seen him, in Kanto, he had cloned all of Ash's Pokémon, which ended with Ash punching him in the stomach and being flash-frozen into rock. He had been revived later. The second time he had seen him had been in Mount Quena in Johto, he had tossed the Legendary into a lake with healing properties and helped him defeat Team Rocket.

All this ran through Ash's mind when he saw the being transform. He smiled broadly.

''Mewtwo!'' he said. Mewtwo smiled in response.

''_Your memory serves you well, Ash._'' he said. Ash smiled again. He carefully put Pikachu down on the ground and ran up to Mewtwo.

Mewtwo threw up a Barrier as soon as Ash got to him, then saw that Ash wasn't attacking him. Instead, he was trying to hug him. Mewtwo decided to let him, releasing the Barrier.

When Ash pulled away from his friend, he was still smiling.

''It's been a while.'' he said. Mewtwo nodded.

''_I see you've grown, Ash._'' he said. It was true. Ash had grown nearly two feet in the five years since they had last met. He was now just as tall as Mewtwo was.

''Hey, sorry for screaming. I didn't recognize you.'' Ash said.

''_It's alright. I didn't expect you to recognize me. I had to use my new form to rescue you because this one wasn't powerful enough. It can't Teleport through as much distance._'' Mewtwo said.

''Really? Your form right now is extremely powerful. How were you able to improve it?'' Ash asked, surprised. Mewtwo smiled.

''_I admit that I am powerful, but this form also has its weaknesses. One of the modifications I made was transferring my extra spinal cord inside my neck, so that it isn't as vulnerable. That also made my Psychic powers amplify more, so I was able to get to you in time. That was part of the reason why I created my new form._''

''You knew about the Genesect?'' Ash asked. Mewtwo nodded.

''_They were recreated from fossils in the same way as I was made. I could sense it._'' he answered, then looked around at their surroundings. ''_I'm not familiar with this area. And I sense that I cannot Teleport as long as I am here._''

''Are you sure?'' Ash asked. By way of answering, Mewtwo's eyes glowed blue like he was going to Teleport, but all that happened was that he swayed a little.

''_It takes away my energies to try._'' Mewtwo concluded.

''So, to get out of here, we have to walk out?'' Ash guessed. Mewtwo nodded. ''Well, then, let's first find out where we are. That could help.''

''_Lead on._'' Mewtwo said, changing to his new form. Ash noticed that Mewtwo was at least seven feet tall with this form. He smiled and began to walk, followed by the Legendary Pokémon.

They asked for directions when they saw a small Pokémon that looked like a green Happy Tree Friend (if you understand this comparison, just know that I wish I had no idea what it meant).

''**You're in the Xernean Forest. Port Maren is a few miles east.**'' it chattered, then jumped through the trees and disappeared. Mewtwo translated the Pokéspeech for Ash.

''What's the Xernean Forest?'' Ash asked. Mewtwo shrugged. The two walked the direction the strange green Pokémon had told them to go.

After walking a few miles, they exited the forest at a beach. To their left they saw Port Maren. There were docks everywhere, all with ships at them, either entering or leaving.

Ash and Mewtwo walked to it.

''Hello. Welcome to Port Maren.'' a voice said from behind them. They turned around. Ash noticed that Mewtwo had transformed into a body that looked almost exactly like a human's.

The person who had spoken was wearing a sea green uniform. Ash thought he looked like he could have been born in the ocean. His hair was a seaweed-green, and stuck up in random directions like Ash's did.

''My name is Lugia.'' the man said. Noticing Ash's and Mewtwo's expressions, he laughed. ''No, not the Legendary Pokémon. Just a person. You'll find a lot of people here with Legendary namesakes. Almost all of us are named for the Element we were born in.''

''Element?'' Ash asked.

Lugia nodded. ''Kalos is separated into four sub-regions, called Elements. The beaches, oceans, lakes, and rivers are in the Water Element. The mountains are in the Fire Element. The main body of the region is in the Earth Element. The atmosphere over the entire region is in the Air Element. Where are you from? From your expressions, I can tell that you're not from around here.'' he said.

''We were just passing through.'' Mewtwo said. ''Which way is it to Unova?''

''If you're from Unova, you're a long way from home.'' Lugia said. ''Unova is a twenty-day plane ride from here. Kalos is practically in the middle of nowhere, geographically speaking.''

Twenty days. How had they gotten so lost just because Ash had screamed when he had seen Mewtwo's new form?

Mewtwo thought for a minute, long enough for Lugia to walk away. When he did, Mewtwo looked at Ash.

''It shouldn't have been possible for us to be here. The path I took to Teleport should have only gone one city away from where you were. Somehow, we ended up here when the Teleport was interrupted. I can't help but feel like there's a reason why my Teleport detoured so greatly.''

''Maybe you went in the wrong direction?'' Ash asked. Mewtwo shrugged.

''Well, whatever the reason, we still need to get out.'' he said. ''Let's go inside the port. Maybe we can find out how to get back to Unova. We still need to help your friends.''

''Who?'' Ash asked. Mewtwo could tell that he wasn't joking. Somehow, Ash had forgotten Iris and Cilan. That thought didn't help Mewtwo's already-edgy mood about this place.

''Never mind.'' he said, and the two walked into the city.

In the city, watching them, was a red orb. It was waiting, as it had been for thousands of years for revenge.


End file.
